In a 5–4 ruling, the Court concluded that Article I of the United States Constitution does not provide Congress with the ability to subject nonconsenting states to private suits for damages in its own courts. In addition, the Court held that Maine was not a consenting party in the suit, and, therefore, the ruling of the Supreme Court of Maine was upheld. Writing for the Court, Justice Anthony Kennedy stated that the United States Constitution provides immunity for nonconsenting states from suits filed by citizens of that state or citizens of any other state, noting that such immunity is often referred to as "Eleventh Amendment Immunity". Such immunity, the Court continued, is necessary to maintain the state sovereignty that lies at the heart of federalism. However, according to Alden v. Maine, "sovereign immunity derives not from the Eleventh Amendment but from the federal structure of the original Constitution itself."

After discussing the Eleventh Amendment, the Court turned to the question of whether Congress has the authority, under Article I of the United States Constitution, to subject nonconsenting states to private suits in their own courts. The majority ruled that Congress has no such authority, under the original unamended Constitution, to abrogate states' sovereign immunity:

Nor can we conclude that the specific Article I powers delegated to Congress necessarily include, by virtue of the Necessary and Proper Clause or otherwise, the incidental authority to subject the States to private suits as a means of achieving objectives otherwise within the scope of the enumerated powers.

However, Congress may abrogate sovereign immunity when the suit is to enforce a statute protecting Fourteenth Amendment rights: "We have held also that in adopting the Fourteenth Amendment, the people required the States to surrender a portion of the sovereignty that had been preserved...Congress may authorize private suits against nonconsenting States pursuant to its §5 enforcement power...When Congress enacts appropriate legislation to enforce this Amendment, see City of Boerne v. Flores, 521 U.S. 507 (1997), federal interests are paramount"

The majority stated that the Supremacy Clause of the Constitution only applies to pieces of legislation that fit within its design. Therefore, any law passed by Congress pursuant to Article I that seeks to subject states to suit would violate the original, unamended Constitution. However, states do not have sovereign immunity if Congress is enforcing the Fourteenth Amendment. See, for example, Fitzpatrick v. Bitzer (1976).

Justice David Souter's dissent argued that the concept of sovereign immunity had been misapplied by the majority. Souter continued by noting that the idea of sovereign immunity was unclear during the period of the Constitution’s ratification. In addition, he argued, the Framers would certainly have not expected the idea to remain static over numerous years.

In addition, Souter argued that the FLSA was national in scope and, as a result, did not violate the principle of federalism as argued by the majority. Souter also argued that the claim the FLSA was unconstitutional was spurious. Such thinking, he argued, could only be reached based upon the misguided notion of sovereign immunity and notion of federalism the majority had used in reaching its decision.

Alden represents an extension of the Court’s 1996 ruling in Seminole Tribe v. Florida, which had held that Congress cannot use its powers under Article I of the Constitution to subject unconsenting states to suit in federal court. Alden holds that Congress cannot use its Article I powers to subject unconsenting states to suit in state court. Later, in Central Virginia Community College v. Katz (2006), the Court would narrow the scope of its previous sovereign immunity rulings, and hold that Congress could use the Bankruptcy Clause of Article I to abrogate state sovereign immunity.